Fig. 4: Prioritised candidate lncRNAs are detectable in early-stage disease.
From: Discovery of prognostic lncRNAs in colorectal cancer using spatial transcriptomics
A Overview of patient cohort for HCR-FISH. Patient 1 = Sigmoid colon primary tumour (stage IIA at first diagnosis), metachronous second primary in ascending colon with associated synchronous metastasis to right lung, upper lobe. Patient 2 = Sigmoid colon primary tumour (stage IVa), synchronous metastasis to para-aortic lymph node. Patient 3 = Recto-sigmoid colon primary tumour (stage IIA at first diagnosis), metachronous second primary in descending colon with associated synchronous metastasis to right lung, middle lobe. Patient 4 = Rectal tumour (stage IIA), metachronous metastasis to the left lung, lower lobe. Patient 5 = Ascending colon primary tumour (stage IV), synchronous metastasis to retroperitoneum. Patient 6 = Mid-ascending colon primary tumour (stage IVb), synchronous metastasis to omentum. Patient 7 = Caecal primary tumour (stage IVa), synchronous metastasis to Liver segments 5 and 6. B Overview of amplification of FISH signal using HCR. C Representative HCR–FISH signal for LINC01978 in Patient 7 primary tumour (left panel = DAPI nuclear staining, left-middle panel = RNA–FISH signal, right-middle panel = MALAT1 positive control expression, right panel = merge). D Representative HCR–FISH signal for PLAC4 in Patient 2 omentum metastasis (left panel = DAPI nuclear staining, left-middle panel = RNA-FISH signal, right-middle panel = MALAT1 positive control expression, right panel = merge). E Representative HCR-FISH signal for LINC01303 in Patient 6 liver metastasis (left panel = DAPI nuclear staining, left-middle panel = RNA–FISH signal, right-middle panel = MALAT1 positive control expression, right panel = merge). F Quantification of HCR-FISH signal for LINC01978. G Quantification of HCR-FISH signal for PLAC4. H Quantification of HCR-FISH signal for LINC01303. Scale bar = 100 µm for all images. DAPI stain denotes nuclei. Met = Metastasis. Rec = Disease recurrence (second metachronous primary). Error bars = mean ± SEM. Tested using a Kruskal–Wallis test for non-parametric data, with Dunn’s post-hoc test for multiple comparisons. * = padj < 0.05. Image created with Biorender.com.
